Last updated: 2019-06-22

Checks: 2 0

Knit directory: BUS_notebooks_R/

This reproducible R Markdown analysis was created with workflowr (version 1.4.0). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.


Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.

Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility. The version displayed above was the version of the Git repository at the time these results were generated.

Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use wflow_publish or wflow_git_commit). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:


Ignored files:
    Ignored:    .Rhistory
    Ignored:    .Rproj.user/
    Ignored:    BUS_notebooks_R.Rproj
    Ignored:    analysis/10xv3_cache/
    Ignored:    data/whitelist_v3.txt.gz
    Ignored:    output/out_pbmc1k/

Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.


These are the previous versions of the R Markdown and HTML files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view them.

File Version Author Date Message
Rmd b208bf2 Lambda Moses 2019-06-22 Added images to index page
html cfd1e88 Lambda Moses 2019-06-22 Build site.
Rmd cdf4749 Lambda Moses 2019-06-22 Added link to kallisto bus paper
html 602b4f6 Lambda Moses 2019-06-22 Build site.
Rmd 5fe6abd Lambda Moses 2019-06-22 Updated index page for new notebooks
html 87d15f5 Lambda Moses 2019-02-14 Build site.
Rmd 8d9fe9a Lambda Moses 2019-02-14 More detailed explanations for kallisto bus workshop
html b7b21a0 Lambda Moses 2019-02-02 Build site.
Rmd c7ecb56 Lambda Moses 2019-02-02 Added BUSpaRse installation link and note
html 85a5770 Lambda Moses 2018-12-14 Build site.
Rmd ca1d6ce Lambda Moses 2018-12-14 Clean up
html 6276894 Lambda Moses 2018-12-14 Build site.
html 1cc5f8a Lambda Moses 2018-12-14 Build site.
Rmd 03c3319 Lambda Moses 2018-12-14 Changed site name
html db70187 Lambda Moses 2018-12-14 Build site.
Rmd b67fc92 Lambda Moses 2018-12-14 Added 10xv3 notebook and further elaboration to 10xv2 notebook
html 064264a Lambda Moses 2018-12-14 Build site.
Rmd d5d64e9 Lambda Moses 2018-12-14 Added installation instruction
html f5616a8 Lambda Moses 2018-12-14 Build site.
Rmd 0dc76a9 Lambda Moses 2018-12-14 Changed to new url
html 540134b Lambda Moses 2018-12-14 Build site.
Rmd e40da79 Lambda Moses 2018-12-14 Changed URL as this repo is transferred to BUStools
html fff442d Lambda Moses 2018-12-14 Build site.
Rmd 695e202 Lambda Moses 2018-12-14 Changed name to BUSpaRse
html 9209390 Lambda Moses 2018-12-14 Update website
Rmd 37238e5 Lambda Moses 2018-12-14 Link to this GitHub repo on the website
html 2da3b35 Lambda Moses 2018-12-14 Build site.
Rmd 1fc3e91 Lambda Moses 2018-12-14 Publish 10xv2 notebook
Rmd 55164fb Lambda Moses 2018-12-14 Start workflowr project.

bustools R notebooks

This repository has example notebooks that demonstrate usage of kallisto bus to generate gene count or (transcript compatibility count) TCC matrices from FASTQ files and some basic downstream analyses. To run the notebooks, please install kallisto, bustools, and the BUSpaRse R package.

Notebooks

1k 1:1 Mixture of Fresh Frozen Human (HEK293T) and Mouse (NIH3T3) Cells (10x v2 chemistry); demonstration of bustools


1k PBMCs from a Healthy Donor (10x v3 chemistry); demonstration of TENxBUSData and BUSpaRse


RNA velocity with 10k E18 mouse neurons from 10x (coming soon)

Differential expression with equivalence classes in TCC matrix (coming soon)